Sequence
atgc intronic sequence ATGC exonic sequence...ttgaagacaacaatgagtagtagttttctccctcatctagaaaattgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
Basic information
species | Glycine max |
transcript | GLYMA06G10540.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 12
--ttgaagacaa---caatgagtagtagttttctccctcatctagaaaattgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
| || | | || | | || | |||| | || | | | | ||||| ||||| | |||||| | || | || ||| ||||| |||||||| |||||||| |||||||| || ||||| || ||||||||||| || || || ||||| || ||| |||| ||||| |||||
atctaaatcctaatccatcaatctctggtcatacaactcacgttgatgtatcgagactagtggctttta-tgtttcttcatattaatttatttggt----tgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACA
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 13
ttgaagacaacaatgagtagtagttttctccctcatctagaaaattgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
| || |||| | || | || | ||| | ||| | || | | ||||||| | |||||| | | || | ||||| ||||| || ||| | || | |||||||||||||| |||||||||||||||||||||||||| | ||||| || |||| ||||| |||||||||
--gtaggttttaatgcattgt-gcttgcatattcagaaaataaaatagaaaatcttgtgccataatgttc--attttgtaatttct-tattgaat--cagGCAATTGCCAAGGATTCTGTTCTGTCAAGATGTAAAATAATTGCAGAGCCTTGGGATTGTGGAGGATTATATCTAGTCGGGAAGTTTCCAAATTGGGATA
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 13
-ttgaagacaacaatgagtagtagttttctccctcatctagaaaattgagaatt-tataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
|| | || ||| | | | | | ||||| || | | || | ||| || | |||||| | | | |||| ||||||||||||| | | ||||| ||||||||||||||||| |||||||||||||| || || || |||||||| || ||||| ||||||||||
aatgga-acgtcaaaaaatgatgaaaattggtcatgctaagaaagggaagcttggtgtagaattttttgcagataccttacgattttt-tttaatggaccagGAAATTGCTAAAGATGATATCCTGTCAAGGTGTAAAATTATTGCAGAACCTTGGGATTGTGGTGGCCTTTACCTTGTTGGAAGGTTTCCAAATTGGGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
aactaat putative branch site (score: 2)
tttttatgttctttt CT-rich tract
atttataaattttaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaagacaacaatgagtagtagttttctccctcatctagaaaattgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - caatgag
- - - - - - - - - - - - - -ctccctc